[miso-users] miso read-len parameter for pairedEnd reads with different lengths

[Sol Katzman]

Dear Yarden,

I have pairedEnd Illumina data that I mapped with tophat. Due to a power outage,
read2 was truncated, so that I have:
  read1=75bp
  read2=58bp

Since there is only a single (required) --read-len parameter for run_miso.py,
is it possible to run miso (exon-centric analysis) on the tophat bams and get
(reasonably) correct results?

If so, what should I use for --read-len?

If not, I will either
a) just run miso with singleEnd (read1 only) bams
b) trim the reads and re-map with tophat using 58x58bp

Thanks,
/Sol.